Freesurfer

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30132 discussions

cvs_register then mri_vol2vol
by Barron, Daniel S 08 Aug '13

08 Aug '13

Hi Freesurfers (Lilla), I'm running v5.1.0 on a Mac trying to apply a cvs morph via the following function: mri_vol2vol --targ cvs_avg35_inMNI152 --m3z $SUBJECTS_DIR/NC001/cvs_avg35_inMNI152/combined_tocvs_avg35_inMNI152_elreg_afteraseg-norm.m3z --noDefM3zPath --mov $SUBJECTS_DIR/NC001/labels/lh.hipp.nii.gz --o $SUBJECTS_DIR/NC001/labels2cvs/lh.hipp2cvsMNI152.nii.gz --interp nearest --no-save-reg Using the m3z file as it is; no assumed location. movvol /media/users/barrond/NYU/Freesurfer/NC001/labels/lh.hipp.nii.gz targvol cvs_avg35_inMNI152 outvol /media/users/barrond/NYU/Freesurfer/NC001/labels2cvs/lh.hipp2cvsMNI152.nii.gz invert 0 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Morphing InvertMorph 0 Synth 0 SynthSeed 1375994175 corRead(): can't open file /media/users/barrond/NYU/Freesurfer/cvs_avg35_inMNI152/COR-.info I don't know what "COR-.info" is or how to make it. Could someone please point me in the right direction? Cheers, Daniel

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Re: [Freesurfer] trac-all inquiry
by Soto, David 08 Aug '13

08 Aug '13

Hi - further to my prior email find attached please a clean version of the log file - without the append of previous attempts as you can see there are no errors in the log although as i said the last line in the Terminal said Segmentation fault (core dumped) cheers ds http://www1.imperial.ac.uk/medicine/people/d.soto/ ________________________________________ From: Soto, David Sent: 07 August 2013 23:47 To: Anastasia Yendiki Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] trac-all inquiry Hi Anastasia, I checked the becs and bvals files, there was a bug in the transposition of the columns into 3 rows in the bvecs. But i still have problems.. I rerun trac-all -prep and seemed fine but ended with a Segmentation fault (core dumped) which however is not present in the last line of the trac-all.log (Attached). Writing output files to /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_* Writing spline volume to /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_cpts_5.nii.gz Segmentation fault (core dumped) Just in case I tried trac-all -bedp complains like these below, any advise appreciated, cheers - ds /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/diffree/tracula02ST.txt -bedp INFO: SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui INFO: Diffusion root is /home/dsoto/Documents/fmri/rsdtianawmgui Actual FREESURFER_HOME /usr/local/freesurfer WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected http://www1.imperial.ac.uk/medicine/people/d.soto/ ________________________________________ From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] Sent: 07 August 2013 17:22 To: Soto, David Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: RE: [Freesurfer] trac-all inquiry Hi David - Every time you run trac-all, the results get appended to this file, so you need to look for error messages only in the more recent invocation of trac-all. The first error there seems to be: Error: bvecs and bvals don't have the same number of entries Do you have the same number of b-values and gradient vectors and volumes in your DWI series? a.y On Tue, 6 Aug 2013, Soto, David wrote: > hi > > I upgraded to FS 5.3 but still encountering issues with > trac-all prep. > > The log is attached, things I noted after inspecting it > > 1) INFO: FreeSurfer build stamps do not match > Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 > Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 > > 2) Error: input image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb not valid > 3) Image Exception : #22 :: ERROR: Could not open image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain > 4) Image Exception : #22 :: ERROR: Could not open image > /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/White-Matter++. > 5) ERROR: Could not read /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_FA.nii.gz > but despite all this it says: > trac-preproc finished without error at Tue Aug 6 21:27:30 BST 2013 > > thanks for your help > > cheers > ds > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > > > > ________________________________________ > From: Anastasia Yendiki [ayendiki(a)nmr.mgh.harvard.edu] > Sent: 06 August 2013 19:30 > To: Soto, David > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: RE: [Freesurfer] trac-all inquiry > > I see, you're using the old version of tracula (from freesurfer 5.1). In > that version, you had to define the number of low-b images in the > configuration file. I strongly recommend updating to freesurfer 5.3. A lot > of things have improved in tracula since then. > > Also, in the future please attach any log files as separate attachments > instead of pasting them into the body of your email - this causes the body > of the email to exceed the limit allowable on the list. > > Thanks, > a.y > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > >

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surface upside down, wrong hemis, nouveau error
by Dewitt, Iain (NIH/NIDCD) [F] 07 Aug '13

07 Aug '13

Dear FreeSurfer community, I have a newly installed version of FreeSurfer: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 running on Red Hat Enterprise Linux 6.4. When I load a surface in tksurfer, eg: tksurfer fsaverage5 lh smoothwm the wrong hemisphere loads and the surface is upside down (see attached image). Further, when I try to select a vertex on the surface, there is no alignment between the pointer and the vertex ultimately selected. For instance, as seen in the attached image, when I click on STG, the vertex highlighted is in the central sulcus. Terminal output is below. I get similar behavior for other surfaces and other pre-installed subjects. The only error message I am getting is: libGL error: failed to load driver: nouveau libGL error: Try again with LIBGL_DEBUG=verbose for more details. Nouveau appears to be installed: [31] /sbin/lspci -v -s `/sbin/lspci | awk '/VGA/{print $1}'` 05:00.0 VGA compatible controller: NVIDIA Corporation GF116 [GeForce GTX 550 Ti] (rev a1) (prog-if 00 [VGA controller]) Subsystem: eVga.com. Corp. Device 1559 Flags: bus master, fast devsel, latency 0, IRQ 30 Memory at f8000000 (32-bit, non-prefetchable) [size=32M] Memory at d8000000 (64-bit, prefetchable) [size=128M] Memory at d4000000 (64-bit, prefetchable) [size=64M] I/O ports at ec00 [size=128] Expansion ROM at f7f80000 [disabled] [size=512K] Capabilities: <access denied> Kernel driver in use: nouveau Kernel modules: nouveau, nvidiafb Any thoughts on what else I should check or what might be going wrong? cheers Iain [20] tksurfer fsaverage5 lh smoothwm subject is fsaverage5 hemi is lh surface is smoothwm surfer: current subjects dir: /home/dewitt/mrdata/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/dewitt checking for nofix files in 'smoothwm' Reading image info (/home/dewitt/mrdata/freesurfer/subjects/fsaverage5) Reading /home/dewitt/mrdata/freesurfer/subjects/fsaverage5/mri/orig.mgz surfer: Reading header info from /home/dewitt/mrdata/freesurfer/subjects/fsaverage5/mri/orig.mgz surfer: vertices=10242, faces=20480 surfer: single buffered window surfer: tkoInitWindow(fsaverage5) libGL error: failed to load driver: nouveau libGL error: Try again with LIBGL_DEBUG=verbose for more details. surfer: using interface /home/dewitt/apps/freesurfer/tktools/tksurfer.tcl Reading /home/dewitt/apps/freesurfer/tktools/tkm_common.tcl Reading /home/dewitt/apps/freesurfer/tktools/tkm_wrappers.tcl Reading /home/dewitt/apps/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/dewitt/apps/freesurfer/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % ----------------------------------- selected vertex 6123 out of 10242 current -47.84 -8.78 45.57 orig -49.76 -9.85 46.75 pial 0.00 0.00 0.00 white -49.73 -9.60 46.90 inflated 0.00 0.00 0.00 normals -0.68 -0.66 0.32 nneighbors 6 ripflag 0 surfer: dmin=1.2521, vno=6123, x=-47.8367, y=-8.7830, z=45.5727 surfer: curv=0.000000, fs=0.000000 surfer: val=0.000000, val2=0.000000 surfer: amp=0.000000, angle=0.000000 deg (0.000000) surfer: vertex 6123 marked (curv=0.000000, stat=0.000000) x = (-47.8, -8.8, 45.6), n = (-0.7, -0.7, 0.3).

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Different results in surface and volume analyses
by Emily Boeke 07 Aug '13

07 Aug '13

Hello everyone, I am looking at a visual stimulus vs fixation contrast in my individual subjects' data to make sure we are seeing normal activation there. If I look at the surface data in tksurfer, I see activation in the occipital cortex, but in the mni305 analysis, there is no activation in this region. These are the preprocess , mkanalysis, and selxavg commands I used for the surface vs. mni305: preproc-sess -s amur_dss -df sesspar -per-run -fwhm 5 -sliceorder down -surface fsaverage lhrh -mni305-2mm -fsd cond mkanalysis-sess -fsd cond -surface fsaverage lh -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.lh -per-run -nskip 4 -stc down mkanalysis-sess -fsd cond -surface fsaverage rh -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.rh -per-run -nskip 4 -stc down mkanalysis-sess -fsd cond -mni305 2 -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.mni305 -per-run -nskip 4 -stc down selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.lh selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.rh selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.mni305 Why might we be seeing this activation on the surface map but not the volume one? Thanks! Emily

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error when using selxavg3-sess in retinotopy analysis
by Sepide Movaghati 07 Aug '13

07 Aug '13

Hi, I followed the steps for doing the retinotopy analysis. At the end I made my analysis as follows: mkanalysis-sess -a Retinotopy_ZY -surface self lh -TR 2 -retinotopy 36 -paradigm rtopy.par -fsd bold -fwhm 5 and then execute selxavg3-sess: selxavg3-sess –a Retinotopy_ZY –s session1 then I got this error which I do not how to solve it: outtop = /export01/data/sepid/subjects/ZY Extension format = nii.gz Error using fscanf Invalid file identifier. Use fopen to generate a valid file identifier. Error in flac_customize (line 47) flacnew.sourcesubject = fscanf(fp,'%s',1); Error in fast_selxavg3 (line 65) flac0 = flac_customize(flac0); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n I would appreciate if you help me through this. Regards, Sepide - I I - a

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Curvature, cortical thickness, LGI and artifacts
by Erin Browning 07 Aug '13

07 Aug '13

Hello-- Our dataset has 130ish scans with a bad temporal lobe artifact and a minor parietal lobe artifact. This artifact has affected the normalization and thus the white matter/gray matter selection, which we've manually fixed. However, the temporal lobe artifact is bad enough that chunks of data are missing in the surfaces. How will this affect curvature and LGI? We saw we can constrain our cortical thickness analyses to an ROI using mri_glmfit. Can we do this with curvature and LGI, and will having chunks of data missing affect readings elsewhere in the brain? Thank you, Erin Browning

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flip hemisphere of manual label
by Jonathan DuBois 07 Aug '13

07 Aug '13

Hi, Is there a way to transpose a manual surface label in fsaverage space onto the contralateral hemisphere? With tksurfer it opens in the opposite hemisphere but it does not correspond to the contralateral region. Thanks in advance. Best, Jonathan

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Re: [Freesurfer] Tracula question
by Anastasia Yendiki 07 Aug '13

07 Aug '13

Hi Alan - Try removing the "\" character from the end of the dcmlist definition. That's a change of line character. a.y On Wed, 7 Aug 2013, Alan Francis wrote: > Hi Anastasia: > > Here is the trac-all log. Please find attached the dmrirc file. > > csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep > -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107 > > Too many ('s. > ERROR: must specify as many DWI dicoms as subjects > > Thank you so much. > > Alan > > > On Wed, Aug 7, 2013 at 12:32 PM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Yes, please attach the dmrirc and trac-all.log. Thanks! > > a.y > > On Wed, 7 Aug 2013, Alan Francis wrote: > > Hi Anastasia: > > For one brain I got this error message : > > csh::alanf@cerebro > [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all > -prep > -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107 > > Too many ('s. > ERROR: must specify as many DWI dicoms as subjects > > I tried specifying the exact number of DWI dicoms but it is not working. Should I send you my > dmrirc for this brain? > > thanks, > > Alan > > > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > >

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set message
by Heather L. Urry 07 Aug '13

07 Aug '13

Hi folks, When issuing a recon-all command, I'm seeing the following message: set: Variable name must contain alphanumeric characters recon-all stalls and doesn't move forward (doesn't even create the subject directory). I'm using Freesurfer 5.3.0 (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu 12.04.2. In fact, we just upgraded to this version of Ubuntu from an older version of Mandriva and to this latest version of Freesurfer. recon-all did not produce this message before these two upgrades. Any help you can offer would be most appreciated! Thanks in advance. Best, Heather -- Heather L. Urry, Ph.D. Department of Psychology Tufts University 490 Boston Avenue Medford, MA 02155 email: heather.urry(a)tufts.edu phone: 617-627-3733 fax: 617-627-3181 http://ase.tufts.edu/psychology/ebbl

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5.3.0 patch
by Moran Cohn 07 Aug '13

07 Aug '13

Dear Freesurfer experts, I recently installed the stable 5.3.0 version of Freesurfer (CentOS 4, 64-bit) and encountered the known problem with the missing ribbon.mgz file when running -autorecon1 -autorecon2. I wonder how I can obtain the patch mentioned for this problem in the release notes, and would be very thankful for your help. Kind regards, Moran Cohn ________________________________ Dit e-mailbericht is alleen bestemd voor de geadresseerde(n). Het kan informatie bevatten die persoonlijk is en niet openbaar mag worden gemaakt krachtens wet- of regelgeving. Gebruik door anderen is niet toegestaan. Indien u niet de geadresseerde(n) bent, wordt u verzocht de verzender hiervan op de hoogte te stellen en het bericht te verwijderen

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